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Computer Vision REU Week 12 Adam Kavanaugh. Recap from Last Time Began work with a blurring method to improve mask generation and background removal accuracy.

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Presentation on theme: "Computer Vision REU Week 12 Adam Kavanaugh. Recap from Last Time Began work with a blurring method to improve mask generation and background removal accuracy."— Presentation transcript:

1 Computer Vision REU Week 12 Adam Kavanaugh

2 Recap from Last Time Began work with a blurring method to improve mask generation and background removal accuracy Began work with a blurring method to improve mask generation and background removal accuracy Found that only 30/71 slides were having brain slices cut from them with previous “Slicer” implementation Found that only 30/71 slides were having brain slices cut from them with previous “Slicer” implementation As of Friday, “Phase 2” is on hold pending Dr. Lobo’s approval. As of Friday, “Phase 2” is on hold pending Dr. Lobo’s approval.

3 Blurring the Database In an attempt to improve the ability of the slicer to extract brains from the slides, I applied a blur to the D3 level of all the slides. In an attempt to improve the ability of the slicer to extract brains from the slides, I applied a blur to the D3 level of all the slides. Blur was applied at Sigma values of 1, 2 and 3 to find which of the 3 values was best suited for this purpose. Blur was applied at Sigma values of 1, 2 and 3 to find which of the 3 values was best suited for this purpose.

4 Sigma 3: Analysis At Sigma 3, slice cuts improved dramatically on the very noisy slides At Sigma 3, slice cuts improved dramatically on the very noisy slides However, most cuts were not usable as they merged together multiple brains into a single mask. However, most cuts were not usable as they merged together multiple brains into a single mask. Extracted slices from 70/71 slides. Extracted slices from 70/71 slides.

5 Sigma 2: Analysis At Sigma 2, merging of multiple brains becomes less of a factor, but this trades off with the loss some slides all together as well as a loss of detail around edges. At Sigma 2, merging of multiple brains becomes less of a factor, but this trades off with the loss some slides all together as well as a loss of detail around edges. However, this resulted in more “useable” brain slices than at the Sigma 3 level. However, this resulted in more “useable” brain slices than at the Sigma 3 level. Extracted slices from 68/71 slides Extracted slices from 68/71 slides

6 Sigma 1: Analysis Best overall sigma value for the D3 image level. Best overall sigma value for the D3 image level. Least amount of combined brain slices, while still cleaning up the background enough to make removal very smooth. Least amount of combined brain slices, while still cleaning up the background enough to make removal very smooth. More defined masks than Sigma 2 level More defined masks than Sigma 2 level Extracted slices from 70/71 slides, with the highest overall slice count from most slides Extracted slices from 70/71 slides, with the highest overall slice count from most slides

7 Original D3

8 Without Blur

9 Sigma 3 Example

10 Sigma 2 Example

11 Sigma 1 Example

12 Overall Blur Effect on Input Half of the data slides had a moderate to high level of noise and other background problems. Half of the data slides had a moderate to high level of noise and other background problems. Applying a blur to the D3 level smoothed out much of this noise. Applying a blur to the D3 level smoothed out much of this noise. Sigma 1 worked best due to the decreased detail at the D3 level which caused many brains to be merged Sigma 1 worked best due to the decreased detail at the D3 level which caused many brains to be merged

13 From Friday.. Devastation Struck! Devastation Struck! Other efforts put on hold. Other efforts put on hold. Worked with Dan over the weekend and on Monday to resolve the issue with the matcher. Worked with Dan over the weekend and on Monday to resolve the issue with the matcher. Current status: Stable Condition, Recovered. Current status: Stable Condition, Recovered.

14 Some Matching Tests In support of Dan’s efforts I got his full system and modified it for my testing purposes. In support of Dan’s efforts I got his full system and modified it for my testing purposes. At the time he was testing different threshold levels starting from 33% and moving Up At the time he was testing different threshold levels starting from 33% and moving Up I began at the top with 100% and also tested at 90% I began at the top with 100% and also tested at 90%

15 Full Pixel Allowance Matcher results on test query of slide MnSOD: Matcher results on test query of slide MnSOD: Top 6 slide matches: Top 6 slide matches: 1) MnSOD [ ] 1) MnSOD [ ] 2) MnSOD [ ] 2) MnSOD [ ] 3) MnSOD [ ] 3) MnSOD [ ] 4) MnSOD [ ] 4) MnSOD [ ] 5) BAPP-LPSLesion-6-2 [ ] 5) BAPP-LPSLesion-6-2 [ ] 6) MnSOD [ ] 6) MnSOD [ ]

16 90% Pixel Allowance Same test using a slice from MnSOD: Same test using a slice from MnSOD: Top 6 results: Top 6 results: 1) MnSOD [ ] 1) MnSOD [ ] 2) MnSOD [ ] 2) MnSOD [ ] 3) MnSOD [ ] 3) MnSOD [ ] 4) MnSOD [ ] 4) MnSOD [ ] 5) MnSOD [ ] 5) MnSOD [ ] 6) MnSOD [ ]* 6) MnSOD [ ]* *MnSOD matches continue through top 9 *MnSOD matches continue through top 9

17 Matcher Results and More As of today, matcher seems to be back up to quality and providing the same, if not better results than we demonstrated previously As of today, matcher seems to be back up to quality and providing the same, if not better results than we demonstrated previously Look for a more detailed and in-depth analysis of these and more matcher results on Friday when Dan presents his findings. Look for a more detailed and in-depth analysis of these and more matcher results on Friday when Dan presents his findings.

18 The Fate of Blur Currently, the mask growing technique that Dan has developed works well enough for our purposes in cutting out brain slices. Currently, the mask growing technique that Dan has developed works well enough for our purposes in cutting out brain slices. If another matching criteria is needed, then using the blur to produce the masks might become important due to more detailed masks. If another matching criteria is needed, then using the blur to produce the masks might become important due to more detailed masks.

19 Moving Forward Continue making adjustments to the 2D system to help bring it closer to finalization. Continue making adjustments to the 2D system to help bring it closer to finalization. Familiarize myself with the 3D system so as to begin work sorting out the problem presented to us in Phase 2: “Brain Slicer 2: This Time With Depth!” Familiarize myself with the 3D system so as to begin work sorting out the problem presented to us in Phase 2: “Brain Slicer 2: This Time With Depth!”


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